| Previous changeset 37:7adde511daa1 (2024-02-29) Next changeset 39:bc57164eb270 (2024-03-01) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767 |
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modified:
__pycache__/jbrowse2.cpython-310.pyc autogenJB2.py jbrowse2.py jbrowse2.xml |
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| diff -r 7adde511daa1 -r 07849bf248e3 __pycache__/jbrowse2.cpython-310.pyc |
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| Binary file __pycache__/jbrowse2.cpython-310.pyc has changed |
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| diff -r 7adde511daa1 -r 07849bf248e3 autogenJB2.py --- a/autogenJB2.py Thu Feb 29 00:51:45 2024 +0000 +++ b/autogenJB2.py Fri Mar 01 00:40:38 2024 +0000 |
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| @@ -109,9 +109,9 @@ } } elif trext == 'bam': - track_conf = {"conf": {"options": {"bam": {"bam_indices": {"bam_index": track[3]}}}}} + track_conf = {"conf": {"options": {"bam": {"bam_index": track[3]}}}} elif trext == 'cram': - track_conf = {"conf": {"options": {"cram": {"cram_indices": {"cram_index": track[3]}}}}} + track_conf = {"conf": {"options": {"cram": {"cram_index": track[3]}}}} else: track_conf = {} track_conf["format"] = trext |
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| diff -r 7adde511daa1 -r 07849bf248e3 jbrowse2.py --- a/jbrowse2.py Thu Feb 29 00:51:45 2024 +0000 +++ b/jbrowse2.py Fri Mar 01 00:40:38 2024 +0000 |
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| @@ -22,7 +22,7 @@ TODAY = datetime.datetime.now().strftime("%Y-%m-%d") GALAXY_INFRASTRUCTURE_URL = None -JB2REL = "v2.10.1" + # version pinned for cloning mapped_chars = { @@ -374,9 +374,10 @@ class JbrowseConnector(object): - def __init__(self, outdir, genomes): + def __init__(self, outdir, jbrowse2path, genomes): self.giURL = GALAXY_INFRASTRUCTURE_URL self.outdir = outdir + self.jbrowse2path = jbrowse2path os.makedirs(self.outdir, exist_ok=True) self.genome_paths = genomes self.genome_name = None @@ -1308,13 +1309,10 @@ json.dump(self.config_json, config_file, indent=2) def clone_jbrowse(self): - """Clone a JBrowse directory into a destination directory.""" - # dest = os.path.realpath(self.outdir) + """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now """ dest = self.outdir - cmd = ["rm", "-rf", dest + "/*"] - self.subprocess_check_call(cmd) - cmd = ["jbrowse", "create", dest, "-t", JB2VER, "-f"] - self.subprocess_check_call(cmd) + #self.subprocess_check_call(['jbrowse', 'create', dest, '--tag', f"{JB_VER}"]) + shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True) for fn in [ "asset-manifest.json", "favicon.ico", @@ -1323,13 +1321,9 @@ "version.txt", "test_data", ]: - cmd = ["rm", "-rf", os.path.join(self.outdir, fn)] + cmd = ["rm", "-rf", os.path.join(dest, fn)] self.subprocess_check_call(cmd) - cmd = [ - "cp", - os.path.join(INSTALLED_TO, "jb2_webserver.py"), - self.outdir, - ] + cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest] self.subprocess_check_call(cmd) @@ -1349,6 +1343,7 @@ if __name__ == "__main__": parser = argparse.ArgumentParser(description="", epilog="") parser.add_argument("--xml", help="Track Configuration") + parser.add_argument("--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda") parser.add_argument("--outdir", help="Output directory", default="out") parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1") args = parser.parse_args() @@ -1364,6 +1359,7 @@ GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL jc = JbrowseConnector( outdir=args.outdir, + jbrowse2path=args.jbrowse2path, genomes=[ { "path": os.path.realpath(x.attrib["path"]), |
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| diff -r 7adde511daa1 -r 07849bf248e3 jbrowse2.xml --- a/jbrowse2.xml Thu Feb 29 00:51:45 2024 +0000 +++ b/jbrowse2.xml Fri Mar 01 00:40:38 2024 +0000 |
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| @@ -14,7 +14,12 @@ ## Copy the XML file into the directory, mostly for debugging ## but nice if users want to reproduce locally cp '$trackxml' '$output.files_path/galaxy.xml' && + +export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && + +## Once that's done, we run the python script to handle the real work python '$__tool_directory__/jbrowse2.py' +--jbrowse2path \${JBROWSE2_PATH} --outdir '$output.files_path' --xml '$trackxml' && #if $jbgen.zipOut == "true": @@ -356,7 +361,7 @@ <param name="category" value="Default" /> <repeat name="data_tracks"> <conditional name="data_format"> - <param name="data_format_select" value="wiggle"/> + <param name="data_format_select" value="bigwig"/> <param name="annotation" value="bw/merlin.bw"/> </conditional> </repeat> @@ -371,11 +376,10 @@ <has_text text="tool_id"></has_text> <has_text text="trackFile path="></has_text> <has_text text="file_ext="bigwig""></has_text> - <has_text text="format="wiggle""></has_text> + <has_text text="format="bigwig""></has_text> </assert_contents> </output> </test> - <test> <param name="reference_genome|genome_type_select" value="history"/> <param name="reference_genome|genome" value="merlin.fa"/> @@ -710,7 +714,6 @@ </assert_contents> </output> </test> - <!-- TODO add a synteny test --> <!-- TODO add a bam and a cram test --> <!-- TODO add an hic test --> |